In view of the problem that existing studies of ecological reservoir operation focus on the single objective of instream ecological water demand and ignore the restoration of instream natural flow regime, indicators of hydrologic alteration (IHA) were divided into two categories to quantify instream ecological water demand and instream flow regime, respectively, and ecological objectives of minimum instream ecological water shortage and maximum instream fit degree of natural flow regime were determined. Furthermore, a multi-objective reservoir group operation model was constructed by combining the target of out-stream socio-economic water supply, and a case study was carried out of a reservoir group in southern China. The results demonstrate that the optimal balanced operation scheme based on the double ecological objective model not only ensures the guarantee rate of water supply to main out-stream water consumers to exceed 95%, but also makes the guarantee rate of water supply to instream ecological objective water demand to reach 91.67%. The constructed model effectively balances both socio-economic and ecological river environment benefits, while enhancing the instream fit degree of natural flow regime, and it is more conducive to river ecological protection, compared with the model that only considers instream ecological water demand.